Recently, a peruvian historian claimed Peru couldn't be considered a colony because it was a kingdom under the Spanish Empire. You can check this link if you understand spanish and want to read a summary of his ideas. Basically, he says that:
I, personally, don't agree with this point of view and don't think those reasons are enough to call the Viceroyalty of Perú a Kingdom. However, I ask you if it's possible to think of spanish viceroyalties as kingdoms because of these reasons or other that aren't mentioned.
I'm not sure I understand Sánchez-Concha's argument here. How does Peru's title of viceroyalty (which yes, they called it that, that's well established) and the lack of systemic extermination (which we can argue about) make it not a colony? That is an odd definition of colony.
New Spain, Peru and for a time New Grenada were indeed nominally kingdoms, governed on the King's behalf through resident Viceroys - so each was a kingdom and a viceroyalty, odd though it may seem. The Rio de la Plata later became the fourth viceroyalty, but I've never seen it referred to as a kingdom.
As their administration by viceroys indicates, they were dependencies subject to the Spanish Crown and the Council of the Indies. So in a sense it's a formal title, perhaps to impress others, perhaps reflecting their importance, perhaps an improvisation in the face of a new situation. The viceroyalties were subdivided into captaincies-general under audiencias, nominally courts but with legislative functions. Provinces were the next level down.
"Colonies" has two meanings, as dependencies or as settlements for imperial populations - in the first sense it's reasonable enough to describe Spain's American territories as colonies, like those of other countries.
It wouldn't be the last time grand statuses were attached to overseas territories: the only imperial title in the British Empire was that of Empress/Emperor of India, technically outranking the British crown had both not been borne by the same person.